How the Gut Microbiome Influences Everything about Your Health

The human digestive system is inhabited by trillions of microorganisms, collectively referred to as the gut microbiome.

Your gut microbiome regulates many physiological functions, both locally in your gut and systemically in diverse tissues and organs ranging from your heart to your skin. Read on to learn about the numerous ways in which gut microbes impact our health, the consequences of gut microbiome disruption, and simple diet and lifestyle changes that optimize the health of your gut microbiome.

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The Human Body: More Microbial than Human?

The human gut microbiome is made up of trillions of microorganisms that, altogether, contribute an impressive nine million unique genes to your body. In fact, our gut microbes possess 150 times more DNA than what’s found in the rest of our bodies, essentially making us more microbial than human! (1, 2) The human genome and gut microbial genome are collectively referred to as the “hologenome.” (3)

Your gut is closely connected with your digestive health, of course, but your immune system, skin, skeletal system, and even your brain function also depend on a healthy gut microbiome. Find out more in this comprehensive guide to the microbiome. #optimalhealth #chriskresser

The Hologenome Theory: Gut Microbes Shape Evolution

According to the hologenome theory, evolution acts not only on the 23,000 human genes, but on the 9.02 million genes (human and microbial) present in and on the body, as a single entity. Studies of the gut microbiota strongly support this theory, as gut microbes are already known to introduce genetic variation in their hosts through three mechanisms:

1. Horizontal Gene Transfer

Horizontal gene transfer happens when genetic material is transferred between unicellular and multicellular organisms. (And we humans are, of course, multicellular.) Some bacteria and other microorganisms that inhabit the human gut are known to participate in horizontal gene transfer. (4) A fascinating example of horizontal gene transfer within the gut microbiota can be seen in the Japanese, whose gut bacteria have, over the course of evolution, acquired a digestive enzyme from a marine bacterium that helps them efficiently digest seaweed. (5)

2. Microbial Amplification

Microbial amplification refers to the flourishing of some microbial populations and the reduction of others in response to environmental inputs such as diet. Microbes that thrive contribute more of their genetic material to the hologenome, influencing host physiology (in the short term) and evolution (in the long term).

3. Acquisition of New Strains

When your body encounters unfamiliar microbes in an environment, it may acquire those new strains of microorganisms. Over time, these acquisitions increase your microbial gene pool and alter the composition of your hologenome.

The introduction of genetic variation to the human body by gut microbes is vital for evolution and may increase “host fitness”—and remember, you are the host. Conversely, the loss of gut microbial species, a phenomenon happening at an unprecedented rate due to Western dietary and lifestyle habits, harms host fitness (that is, our health) and that of future generations. (6)

What Does a Healthy Gut Microbiome Look Like?

The gut microbiome contains several broad classes of organisms, including bacteria, fungi, viruses, and parasites. Usually, most of these microbes are found in the large intestine, with relatively few microbes found in the stomach and small intestine. While we can’t say with certainty what a “normal” gut microbiome looks like, we are aware of specific microbial species and patterns of colonization that are beneficial. For starters, we know that there are four major phyla of bacteria that compose the gut microbiome: (7)

Bacteroidetes

Firmicutes

Actinobacteria

Proteobacteria

Together, Bacteroidetes and Firmicutes make up 90 percent of total bacterial species in the gut. (8)

We also understand from research that a higher diversity of gut microbes is associated with better health. Genetics, ethnicity, and close social relationships also appear to influence the composition of the gut microbiota. (9, 10, 11)

Residents of the Human Gut Microbiome

The gut microbiome does not contain only bacteria; it is also home to viruses, fungi, and parasites. Listed here are some of the common commensal, opportunistic, and pathogenic microbes found in the human gut:

Commensal Bacteria

The term “commensal bacteria” refers to bacteria that are considered “normal” inhabitants of the human gut. These bacteria include members of Bifidobacterium, Enterococcus, Lactobacillus, and Clostridia. Though some “Clostridia” include harmful microbes such as Clostridium difficile (discussed below), many Clostridia species are beneficial and help maintain gut health. (12)

Opportunistic Bacteria

Opportunistic bacteria are those ordinarily present at low levels in the gut but which can become problematic because they tend to proliferate when beneficial bacteria are depleted. Opportunists include Bacillus, Enterococcus faecalis, Enterococcus faecium, Staphylococcus, and Streptococcus.

Fungi

Fungi are normal inhabitants of the human gut but form a minority of total gut microorganisms. Candida spp., Geotrichum, and Saccharomyces are common opportunistic gut fungi that can overgrow in response to a high carbohydrate intake or antibiotic use.

Gut pathogens can also be viral or parasitic. Adenovirus frequently causes respiratory infections but may also infect the gastrointestinal tract, while norovirus is a trigger for severe, acute vomiting and diarrhea. Parasitic gut pathogens include protozoa such as Cryptosporidium, Entamoeba histolytica, Giardia, and Blastocystis hominis and worms such as Ascaris lumbricoides (roundworm) and Trichuris trichiura (human whipworm).

Bacterial Autoimmune Triggers

In addition to its normal digestive functions, the human gut has to deal with all these microbes! Fortunately, it has a built-in system for regulating levels of gut microbes and protecting against infections, including antimicrobial peptides and microRNA molecules. (17, 18) However, sometimes these systems go awry, resulting in unfavorable changes in the gut microbiome and disrupting its regular processes, outlined in the next section.

What Does the Gut Microbiome Do Within Our Bodies?

A healthy gut plays an important role in maintaining motility in the gastrointestinal tract, supporting a strong gut barrier, and many other functions that are crucial to maintaining your health.

Maintains Gastrointestinal (GI) Motility

Gut microbes support GI motility (digesting and moving food through the GI tract) by regulating neurotransmission throughout the enteric nervous system of the gut. (19) Motor disorders and small intestinal bacterial overgrowth (SIBO) can alter the gut microbiome, which impairs GI motility. This relationship between motility and the microbiome is bidirectional, meaning that an altered microbiome can impact motility and issues with motility can also impact the microbiome.

Supports Gut Barrier Integrity

Gut microbes help maintain the integrity of the gut barrier by stimulating intestinal epithelial cell proliferation (the cells that make up the lining of the intestines) and regulating tight junction proteins, which bind intestinal cells together. (20) They also boost the development of gut-associated lymphoid tissue (GALT), a type of tissue found exclusively in the gut that mediates immunity.

Competes with Pathogens

Gut microbes compete with pathogens for colonization in the human gut; the stronger the commensal microbiota is, the lower the risk of gut infections. (21)

Synthesizes Vitamins

How Does the Gut Microbiome Impact Our Health?

Because the functions of a healthy gut microbiome are so diverse, any number of symptoms can appear due to dysbiosis.

Allergies

Struggling with allergies? Your gut microbes could be to blame. Normally, your gut bacteria are responsible for “teaching” your immune system how to tolerate dietary proteins and environmental allergens such as pollen and dust mites. When the gut microbiota is disrupted, this teaching process is impaired and the body has a negative reaction to allergens, resulting in food and environmental allergies. (26, 27) Ensuring a healthy gut microbiota in expectant mothers and infants may, on the other hand, help prevent the onset of allergic diseases. (28)

Autoimmunity

In addition to influencing autoimmune diseases directly linked to the gut, such as Crohn’s disease and ulcerative colitis, we know from emerging research that the gut microbiota also affects the development of non-intestinal autoimmune disorders, including lupus, multiple sclerosis, and type 1 diabetes. (29)

Bone Health

Could your gut microbiome impact the health of your skeletal system? As it turns out, studies show that there is a crucial link between these two systems. Two of the underlying causes of skeletal issues, such as osteoporosis, are inflammation and nutrient deficiencies. Studies show that, by regulating the body’s inflammatory balance, gut microbes can either promote or inhibit bone loss. A healthy gut microbiome also enhances the absorption of critical bone-building nutrients, including vitamins D and K2, calcium, and magnesium. (30) Supplementation with prebiotic fibers increases bone strength and calcium content by supporting the growth of helpful microbes involved in intestinal calcium absorption. (31)

Brain Function

The gut microbiome influences the brain and neurobehavior via the gut–brain axis, a network of neurons and signaling molecules linking the enteric nervous system of the gut with the central nervous system. Disruptions of the gut microbiome are implicated in autism, ADHD, neurodegenerative diseases, anxiety, and depression. (32, 33, 34, 35, 36) Conversely, restoration of a healthy gut microbiome with prebiotics and probiotics may alleviate symptoms of neurobehavioral and neurodegenerative diseases. (37, 38, 39, 40) These findings strongly suggest that the gut microbiome is a modifiable factor in the development of brain disorders.

Cancer

The gut microbiome may play a critical role in the development of certain cancers, particularly breast and colon cancer. (41, 42) Research indicates that the gut microbiota of women with breast cancer differs significantly from that of healthy women. Gut microbes capable of metabolizing estrogens influence the body’s estrogen levels; too many or too few of these bacteria may drive the development of estrogen-sensitive breast cancer. Furthermore, exposure to estrogen-like compounds—commonly through environmental exposures, like BPA-containing water bottles, other forms of plastic packaging, and cash register receipts—alters the gut microbiome, leading to undesirable changes that may also influence breast cancer development.

The gut microbiome also appears to influence the development of colon cancer. Elevated levels of the sulfur-producing bacterium Bilophila wadsworthia and the opportunistic and pathogenic bacteria Streptococcus bovis, Helicobacter pylori, Bacteroides fragilis, and Clostridium septicum are associated with an increased risk of colon cancer, likely due to the bacteria’s pro-inflammatory effects on colonic tissue. (43)

An individual’s gut microbes may even influence how he or she responds to cancer immunotherapy, according to a recent study published in Translational Cancer Research. (44) Correcting imbalances in the gut microbiome may be crucial for both preventing and treating cancer.

Cardiovascular Disease

Cardiovascular disease, the leading cause of death worldwide, may be mediated by the gut microbiome. There are several ways that gut bacteria may influence cardiovascular health.

Gut dysbiosis causes bacteria to move from the gut lumen into the bloodstream, initiating an inflammatory response that triggers the growth and build-up of arterial plaque (atherosclerosis), which can cause heart attack and stroke. These plaques have been found to contain bacterial DNA identical to that present in the gut, further supporting the notion that gut microbe-induced inflammation contributes to cardiovascular disease. (45, 46)

A special note on TMAO: The precursors for TMAO (such as choline, phosphatidylcholine, and carnitine) are abundant in meat and eggs; this point has been used to support the argument that animal foods cause heart disease. However, epidemiological evidence does not support this theory. (52, 53) Meat consumption may be erroneously linked to TMAO and CVD because of the healthy-user bias. You can read more about my thoughts on TMAO, CVD, and the healthy-user bias here. It is more likely the balance of bacteria in the gut that influences TMAO production and subsequent CVD risk than the consumption of animal products.

The gut microbiome also plays a crucial role in type 2 diabetes. (56) Several studies have shown that opportunistic pathogens are increased while microbes that produce butyrate (a beneficial compound with an anti-inflammatory effect) are decreased in type 2 diabetes. (57) The resulting gut dysbiosis allows the leakage of harmful bacterial metabolites into the circulation, inducing chronic inflammation, an important underlying cause of type 2 diabetes. (58)

Gastrointestinal Health

Not surprisingly, gut microbes play pivotal roles in the development and progression of gastrointestinal disorders, including irritable bowel syndrome (IBS) and SIBO.

In IBS, there is a relative abundance of pro-inflammatory bacteria such as Enterobacteriaceae and reduced levels of Lactobacillus and Bifidobacterium. (59) The incidence of IBS is also higher in people who have experienced protozoan or parasitic infections or bacterial gastroenteritis. (60)

IBS shares some important features with SIBO, including elevated levels of methanogens, which are gut bacteria that produce methane. However, patients with SIBO are unique in that their bacterial imbalance is specifically located in their small intestine. SIBO may also be characterized by elevated levels of hydrogen- or sulfur-producing bacteria. (61)

Inflammatory bowel disease (IBD) patients demonstrate high levels of Caudovirales, an order of viruses known as “tailed bacteriophages,” and marked fungal dysbiosis characterized by elevated levels of Basidiomycota, Ascomycota, and Candida albicans fungi. (62, 63)

Patients with IBS often have gastroesophageal reflux disease, or GERD, and vice versa, suggesting a gut bacterial issue underlying both conditions. (64) H. pylori and SIBO may contribute to these two conditions by increasing intestinal gas production and reducing stomach acid production, respectively. These effects increase pressure on the stomach and impair digestion and may cause reflux of undigested stomach contents into the lower esophagus.

Immunity

Metabolites of beneficial gut bacteria, such as short-chain fatty acids, promote the development of a robust immune system. (65) Gut dysbiosis may impair the immune response, increasing the likelihood of gastrointestinal infections and respiratory infections.

Obesity

An elevated ratio of Firmicutes to Bacteroidetes is associated with an increased risk of being overweight or obese. (66) Dysbiosis may promote obesity by increasing the amount of energy (calories) obtained from the diet, by promoting leaky gut and systemic inflammation, by increasing appetite, and by inflaming the nervous system, leading to impaired satiety mechanisms. (67)

Skin Health

Gut microbes influence the health of our skin by modulating the gut–skin axis, a bidirectional signaling pathway between the gut and skin. (68) Via this axis, gut microbes send signals to the skin that influence inflammation and sebum production, ultimately impacting the development of skin disorders.

Gut dysbiosis is involved in dermatological diseases in humans, evidence shows. Patients with rosacea have a high prevalence of SIBO, and for many, skin symptoms improve with SIBO treatment. (69) Psoriasis patients also harbor dysregulated gut microbiomes and elevated levels of pro-inflammatory cytokines, which may be caused by bacteria moving from the gut into the bloodstream. (70) While human research is ongoing, it’s becoming quite clear that the gut microbiome should not be ignored when treating skin issues.

Thyroid Disorders

The gut microbiome could also be the missing link in your efforts to improve your thyroid function. Alterations in the gut microbiome are linked with hyperthyroidism; while research is lacking in patients with hypothyroidism, common sense tells us that the gut microbiome may also play a role in such cases. (71) Gut dysbiosis may contribute to thyroid disorders by triggering a sustained release of LPS (short for lipopolysaccharide, a naturally occuring fat–sugar compound) into the bloodstream; LPS inhibits iodothyronine deiodinase, the enzyme responsible for converting thyroxine (T4) into the active thyroid hormone triiodothyronine (T3). LPS also decreases the expression of thyroid hormone receptors, which are necessary for mediating the effects of thyroid hormones in the body. (72)

Eight Factors That Disrupt the Gut Microbiome

A plethora of factors in modern-day life disrupts the gut microbiota. Staying aware of these factors can help you make smart diet and lifestyle decisions that will ultimately support your gut microbes and your overall health.

1. Antibiotics

Antibiotic overuse is a pervasive problem that is rapidly changing the human gut microbiota. Just a single course of antibiotics causes rapid and long-lasting changes in the gut microbiome. (73) Antibiotics decimate beneficial gut bacteria while creating space for opportunistic pathogens to proliferate. Antibiotic overuse has also contributed to the meteoric rise of antibiotic-resistant bacteria, which are responsible for serious infections such as MRSA. (74)

2. Non-Antibiotic Pharmaceutical Drugs

Several types of non-antibiotic drugs also have adverse effects on the gut microbiome. Proton-pump inhibitors (PPIs) have significant adverse effects on the gut microbiome, decreasing microbial diversity and increasing opportunistic and pathogenic bacteria such as Streptococcus, Staphylococcus, and E. coli. (75) Antifungal drugs may also skew the composition of the gut microbiome, leading to colonization by drug-resistant fungi. (76) Last but not least, antipsychotic drugs deplete commensal bacteria, particularly the anti-inflammatory bacterium Akkermansia muciniphila. (77)

3. C-Section Birth

The shaping of the gut microbiome begins at birth. Infants delivered vaginally are “seeded” at birth with their mother’s vaginal flora, including beneficial microbes from the Lactobacillus and Prevotella families. Cesarean-section birth, on the other hand, only allows infants to acquire limited bacteria from the surrounding environment (a sterile delivery room), such as the skin of their mother, as well as doctors and nurses. Research shows that C-section babies have a lower gut microbiome diversity compared to babies born vaginally and are also more likely to be colonized by opportunistic pathogens such as Staphylococcus. (78) These changes in the gut microbiomes of C-section babies alter their immune function and may predispose them to allergies, asthma, and obesity, among other health problems, even into adulthood.

What if a C-section birth is unavoidable for legitimate medical reasons? Are there ways to correct the damage done to the infant gut microbiome? New research efforts seek to answer this question. A recent study found that administration of a synbiotic (a prebiotic/probiotic combination) led C-section babies to eventually develop a gut microbiota more reflective of that of infants born vaginally. (79)

5. Genetically Modified Foods

Genetically modified (GMO) foods are the subject of significant controversy in our nation today. Some critics argue that GMOs are responsible for our current epidemics of allergic and gastrointestinal diseases, while GMO advocates quickly dismiss these concerns as “unscientific.” While the jury is still out as to whether GMOs are indeed harmful, a mounting body of evidence indicates that, at the very least, they induce changes in the gut microbiome.

Remember our discussion of horizontal gene transfer earlier? Some startling research shows that GMOs undergo horizontal gene transfer with our own gut microbes; this may adversely affect the gut microbiome, with unknown effects on our long-term health. (83) Furthermore, GMO foods are heavily contaminated by glyphosate, the active ingredient in the controversial herbicide Roundup, which has recently been found to harm the gut microbiome. (84) I recommend avoiding the most common GMO foods—corn, soybean, cottonseed oil, canola oil, potatoes, papaya, and sugar beets. Most of these foods are pretty unhealthy anyway, but if you choose to eat potatoes and papaya, opt for organic.

6. Sleep and Circadian Rhythm Disruption

Sleep deprivation and circadian rhythm disruption are often overlooked but crucial factors that influence the gut microbiome. In animal studies, circadian disruption induced by a reversed light/dark cycle has been found to alter the gut microbiota significantly; in humans, such alterations are caused by shift work and may explain the connection between shift work and metabolic dysfunction. (85, 86)

7. Chronic Stress

Chronic stress doesn’t just detract from your quality of life; it also harms your gut microbiome. In animal studies, chronic psychological stress is associated with reduced bacterial diversity and beneficial gut bacteria. (87) Stress may cause gut microbiome changes through the release of catecholamines and other neuroendocrine hormones that directly modulate microbial growth. (88) Stress also alters oxygenation of the intestine, influencing which types of microbes can survive there. (89)

8. Existing Chronic Infections

Long-term infections with fungal, bacterial, and viral pathogens can change the makeup of the gut microbiome. (90) These infections don’t even need to cause noticeable symptoms. They can lie unnoticed for years, doing serious harm to gut health. Stool testing can uncover any existing infections, even if they’re not causing acute symptoms.

Nine Ways to Support a Healthy Gut Microbiota

If you’re suffering from dysbiosis, you do have options to heal your gut. If you have any existing infections, it’s important that you seek treatment for those, preferably from a Functional Medicine practitioner. Otherwise, by modifying your diet and lifestyle, you can support a healthier microbiota.

1. Eat Enough Dietary Fiber

Whole, nutrient-dense foods promote a healthy gut microbiome. These foods are rich in dietary fiber, which supports the growth of beneficial gut bacteria. (91) Resistant starch, a type of dietary fiber that passes through the small intestine undigested and ultimately feeds beneficial microbes in the large intestine, is particularly good for you. Its consumption is linked to improvements in metabolic and digestive system health. You can learn more about resistant starch in my article “How Resistant Starch Will Help to Make You Healthier and Thinner.”

2. Try Polyphenols

Polyphenol-rich foods, such as blackberries and purple sweet potatoes, increase levels of the anti-inflammatory gut bacterium Akkermansia muciniphila. (92) The metabolites of Akkermansia support a healthy brain and metabolism. (93)

3. Drink Coffee and Tea

Good news for coffee lovers—one of the main chemical compounds found in coffee, chlorogenic acid, increases gut bacterial production of SCFAs. (94) SCFAs, in turn, reduce inflammation and improve blood sugar control. If you’re not a coffee drinker, then you may be happy to hear that tea also benefits the gut microbiome. Several phytochemicals in tea inhibit the growth of gut pathogens such as E. coli and Salmonella typhimurium.

4. Eat Fermented Foods

Fermented foods introduce probiotics to your digestive system, while also improving intestinal barrier function. (95) Kimchi, sauerkraut, and kombucha are easy, delicious ways to add probiotics to your diet. If you tolerate dairy, you may also consider adding full-fat yogurt and kefir.

5. Avoid Harmful Foods

In addition to adding the foods listed above to your diet to support your gut microbiome, you should also remove foods that may be harming it. Refined carbohydrates and industrial seed oils don’t do your gut microbiome any favors and should be avoided. Gluten is another common disruptor of the gut microbiome; gluten sensitivity can be identified through lab testing and/or an elimination diet.

6. Take Probiotics

Research on probiotics has exploded in recent years, with studies assessing their effects on health conditions ranging from major depressive disorder to obesity. Probiotics show promise for alleviating anxiety, depression, and perceived stress. (96) They also improve fasting insulin and hemoglobin A1c in type 2 diabetics and reduce the rate of cold and flu infections in adults. (97, 98) However, no probiotic can cancel out the harmful effects of an unhealthy diet on the gut microbiome, so the intake of dietary fiber, polyphenols, and fermented foods should remain a priority.

9. Exercise

Research shows that physical activity modulates the gut microbiota, enriching the number of beneficial microbes and increasing microbial diversity. (100) High-intensity interval training and aerobic exercise both have beneficial effects on the gut microbiome; endurance activity, however, may have detrimental long-term effects by increasing intestinal permeability and oxidative stress. Importantly, favorable changes in the gut microbiome are reversed when exercise stops, indicating that we must exercise regularly to achieve long-term gut health benefits. (101) To support your gut microbiota, taking care to exercise consistently—without overdoing it—appears to be essential.

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5 Comments

I am curious what your thoughts are on chlorinated water ingested and showered in? Specifically the impact of chlorine and chloramines on the microbiota? I’m studying the soil food web, and we definitely never want to apply chlorinated water directly to compost creating inoculates, plants or the soil. Currently I filter shower, bath, drinking, and garden water – but they are all using plastic filter housings. Also, What is the impact of going to a steam sauna at the Y and potentially ingesting chlorine and chloramines in the lungs – which would be have its own biome? Cheers!

Thanks Chris. I’ve eliminated gluten and dairy from my diet. Focus on nutrient-dense foods, organic fruit and vegetables as much as possible and grass fed (and organic if available) meats and quality seafood. Pretty much follow a Paleo diet and have increased goof fat intake. I’ve added collagen hydrosylate and gelatin, Reishi mushrooms, and Ashwaghanda to aid sleep and gut health. Working with a Functional Medicine Doctor, i’ve treated a parasite and candida, and added zinc and Vitamin B12 to my diet. I also had an iron infusion. I was already taking a good quality probiotic. I’ve added a synbiotic. Exercise – Going to a yoga class 3 times weekly, walking, hill climbs, Chi Gung and now swimming. And i’m felling well and energized. I’m 63. I find your work inspiring and very informative. Thank you.

I am not sure if I struggle with gut dysbiosis. I have chronic adult acne which is totally influenced by what I eat so that makes me wonder if I do. Other than that, I am in excellent health so that also makes me wonder if I don’t! I take Visbiome which is a high potency probiotic. I also eat lots of prebiotics (oats, apples, bananas, etc) and other fibre rich foods. I also enjoy miso regularly as a fermented food. But I also eat lots of bread which I assume is a poor choice.

This is an awesome find, stumbling upon this article is a God send. Do you recommend any particular gut microbiome test to start the healing journey before and after learning the rest of the story kind of help?